Either:
- Go into iTunes, makes sure the album cover is still there. Then Try Syncing.
- Unsync the affected albums and re-sync them
- Uninstall MobileMusicPlayer Flip (it is the main culprit for this problem)

No. Try adding the artwork to the files again. Right click on the songs in iTunes that you want to add artwork to, and click "Get Album Artwork." If that doesn't work, add the artwork to the songs manually, by right clicking the songs, going to the artwork tab, and copy and pasting the artwork in.